[gmx-users] g_bundle!

Alan Dodd anoddlad at yahoo.com
Thu Jun 21 13:29:12 CEST 2007

I've used g_bundle a lot for just this sort of thing.  You need to define the top and bottom of the helix as seperate groups, and define them *very* carefully - it does make a difference how you do it, presumably because g_bundle just plots the axis between the COM of both groups?  I usually define as close to 1 complete turn of the backbone of the helix at each end as possible.
Your output is not surprising, given what you've asked the program for - the axis between two points that precisely overlap ;-)

----- Original Message ----
From: priyanka srivastava <priyankaps4 at yahoo.com>
To: gmx-users at gromacs.org
Sent: Wednesday, June 20, 2007 3:27:42 PM
Subject: [gmx-users] g_bundle!

Dear All,

I want to calculate tilt angle of a peptide inserted
inside the lipid bilayer (i.e. angle between the
helical axis and bilayer normal). From previous posts
I got an idea that g_bundle wud solve my problem.

I am issuing the following on the command line:

g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps

This asks me to "Select a group of top and a group of
bottom atoms"

Group     0 (      System) has 12877 elements
Group     1 (     Protein) has   102 elements
Group     2 (   Protein-H) has    79 elements
Group     3 (     C-alpha) has    10 elements
Group     4 (    Backbone) has    31 elements
Group     5 (   MainChain) has    41 elements
Group     6 (MainChain+Cb) has    49 elements
Group     7 ( MainChain+H) has    54 elements
Group     8 (   SideChain) has    48 elements
Group     9 ( SideChain-H) has    38 elements
Group    10 ( Prot-Masses) has   102 elements

when I chose "1" and "1" it gives all angles as 90,
which is wrong and bun_tiltr is reported as "nan". The
manual says that "the program reads two index groups
and divides both of them in -na parts".
I am a lil confused! what should be my choice here?


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